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PubMed2001

Comparative study and prediction of DNA fragments associated with various elements of the nuclear matrix.

Scaffold/matrix-associated region (S/MAR) sequences are DNA regions that are attached to the nuclear matrix, and participate in many cellular processes. The nuclear matrix is a complex structure consisting of various elements. In this paper we compared frequencies of simple nucleotide motifs in S/MAR sequences and in sequences extracted directly from various nuclear matrix elements, such as nuclear lamina, cores of rosette-like structures, synaptonemal complex. Multivariate linear discriminant analysis revealed significant differences between these sequences. Based on this result we have developed a program, ChrClass (Win/NT version, ftp.bionet.nsc.ru/pub/biology/chrclass/chrclass.zip), for the prediction of the regions associated with various elements of the nuclear matrix in a query sequence. Subsequently, several test samples were analyzed by using two S/MAR prediction programs (a ChrClass and MAR-Finder) and a simple MRS criterion (S/MAR recognition signature) indicating the presence of S/MARs. Some overlap between the predictions of all MAR prediction tools has been found. Simultaneous use of the ChrClass, MRS criterion and MAR-Finder programs may help to obtain a more clearcut picture of S/MAR distribution in a query sequence. In general, our results suggest that the proportion of missed S/MARs is lower for ChrClass, whereas the proportion of wrong S/MARs is lower for MAR-Finder and MRS.

Animals↗
PubMed2003

Complete structure analysis of OR-1746, a complex product of cyclocondensation of arylhydrazomalononitriles containing clusters of protonated and unprotonated nitrogens, by pulsed-field-gradient heteronuclear NMR.

OR-1746, or [4-Ethoxy-6-imino-5-[[4-(4-methyl-6-oxo-1,4,5,6-tetrahydropyridazin-3-yl)phenyl]hydrazono]-5,6-dihydro-1H-pyrimidin-2-ylidene]-[4-(4-methyl-6-oxo-1,4,5,6-tetrahydropyridazin-3-yl)phenylazo]-acetonitrile is the product of the cyclocondensation of two molecules of the arylhydrazomalononitrile levosimendan (CAS registry number [141505-33-1]) with ethanol. OR-1746 is a molecule with a complex structure containing clusters of protonated and unprotonated nitrogens. Its structure was only partially elucidated by elemental analysis and by conventional NMR. However, the presence of many unprotonated nitrogen atoms did not allow the unambiguous assignment of the 1H, 13C and 15N NMR spectra with short-range heterocorrelated techniques, or even with traditional long-range 2D experiments. Pulsed-field-gradient heteronuclear multiple bond coherence sequences (PFG 1H-(13)C and PFG 1H-(15)N) were, therefore, used to fully assign the NMR spectra and elucidate the chemical structure of OR-1746. By using these techniques, long-range couplings between protons and carbons or proton and nitrogen atoms as distant as five bonds in the structure were detected without loosing the signals of the protonated heteroatoms. The long range coupling information provided by the novel NMR experiment can be used effectively in the complete structure determination of complex molecules containing clusters of protonated and unprotonated nitrogens.

Chromatography, High Pressure Liquid↗
PubMed2001

Structure of cephalosporin acylase in complex with glutaryl-7-aminocephalosporanic acid and glutarate: insight into the basis of its substrate specificity.

BACKGROUND: Semisynthetic cephalosporins are primarily synthesized from 7-aminocephalosporanic acid (7-ACA), which is obtained by environmentally toxic chemical deacylation of cephalosporin C (CPC). Thus, the enzymatic conversion of CPC to 7-ACA by cephalosporin acylase (CA) would be of great interest. However, CAs use glutaryl-7-ACA (GL-7-ACA) as a primary substrate and the enzyme has low turnover rates for CPC. RESULTS: The binary complex structures of CA with GL-7-ACA and glutarate (the side-chain of GL-7-ACA) show extensive interactions between the glutaryl moiety of GL-7-ACA and the seven residues that form the side-chain pocket. These interactions explain why the D-alpha-aminoadipyl side-chain of CPC yields a poorer substrate than GL-7-ACA. CONCLUSIONS: This understanding of the nature of substrate specificity may be useful in the design of an enzyme with an improved performance for the conversion of CPC to 7-ACA. Additionally, the catalytic mechanism of the deacylation reaction was revealed by the ligand bound structures.

Catalysis↗
PubMed2004

Catalytic mechanism of guanidinoacetate methyltransferase: crystal structures of guanidinoacetate methyltransferase ternary complexes.

Guanidinoacetate methyltransferase (GAMT) is the enzyme that catalyzes the last step of creatine biosynthesis. The enzyme is found in abundance in the livers of all vertebrates. The intact GAMT from recombinant rat liver has been crystallized with an inhibitor S-adenosylhomocysteine (SAH) and a substrate guanidinoacetate (GAA), and with SAH and an inhibitor guanidine (GUN). These ternary complex structures have been determined at 2.0 A resolution. GAMT has an alpha/beta open-sandwich structure, and the N-terminal section (residues 1-42) covers the active site entrance so that the active site is not visible. SAH has extensive interactions with GAMT through H-bonds and hydrophobic interactions. The guanidino groups of GAA and GUN form two pairs of H-bonds with E45 and D134, respectively. The carboxylate group of GAA interacts with the backbone amide groups of L170 and T171. A model structure of GAMT containing the two substrates (SAM and GAA) was built by attaching a methyl group (C(E)) on S(D) of the bound SAH. On the basis of this model structure, a catalytic mechanism of GAMT is proposed. The active site entrance is opened when the N-terminal section is moved out. GAA and SAM enter the active site and interact with the amino acid residues on the surface of the active site by polar and nonpolar interactions. O(D1) of D134 and C(E) of SAM approach N(E) of GAA from the tetrahedral directions. The O(D1)...N(E) and C(E)...N(E) distances are 2.9 and 2.2 A, respectively. It is proposed that three slightly negatively charged carbonyl oxygen atoms (O of T135, O of C168, and O(B) of GAA) around O(D1) of D134 increase the pK(a) of O(D1) so that O(D1) abstracts the proton on N(E). A strong nucleophile is generated on the deprotonated N(E) of GAA, which abstracts the methyl group (C(E)) from the positively charged S(D) of SAM, and creatine (methyl-GAA) and SAH (demethyl-SAM) are produced. E45, D134, and Y221 mutagenesis studies support the proposed mechanism. A mutagenesis study and the inhibitory mechanism of guanidine analogues support the proposed mechanism.

Animals↗
PubMed2003

Electronic structures of mixed-sandwich complexes of cyclopentadienyl and Hydrotris(pyrazolyl)borate ligands with 3d transition metals.

The electronic and magnetic properties of a series of mixed-sandwich complexes MCp(R)Tp (Cp(R) = Cp or Cp; Tp = hydrotris(pyrazolyl)borate; M = V, Cr, Fe, Co or Ni) have been studied and compared to their homoleptic analogues, MCp(R)(2) and MTp(2). Solid-state magnetic susceptibility measurements and EPR spectroscopic data indicate that complexes with d(3), d(6), and d(8) configurations are similar electronically to their metallocene analogues, except for FeCpTp, which displays a spin equilibrium (S = 0 if S = 2) in solution which was investigated by variable- temperature NMR spectroscopy. The d(2) complex [VCpTp](+) displays magnetic behavior consistent with an orbitally nondegenerate ground state. The d(4) species CrCpTp has a high-spin (S = 2) ground state. The d(7) species CoCpTp is high spin (S = 3/2) whereas its Cp analogue and [NiCpTp](+) are both low-spin (S = 1/2) species. The optical spectra of the d(3), d(6), and d(8) complexes were assigned in a fashion similar to the analogous metallocenes and ligand-field parameters (delta(1) = delta-sigma gap, delta(2) = sigma-pi gap for d-orbitals in axial symmetry) calculated. The analysis shows that for 15-electron species the total ligand-field splitting, delta(TOT), is larger than for their metallocene analogues, whereas for the 18-electron case Delta(TOT) is smaller and for 20-electron systems delta(TOT) is approximately the same. In all cases delta(2) is substantially reduced compared to the metallocenes, and in the majority of cases delta(1) is markedly larger. DFT calculations were performed to investigate further the nature of the ligand environment on the frontier orbitals in these complexes. Orbital energies and compositions were calculated and compared for a series of homoleptic and mixed-sandwich complexes of Ni(II) and across the 1st transition series for MCp(R)Tp species. The ability of Tp (vs Cp) to act as a delta-donor (with respect to the principal molecular axis) imparts significant ligand antibonding character to the delta-orbitals and results in decreased epsilon(pi)-epsilon(delta) values compared to the metallocenes and an increased tendency toward high-spin complexes in the mixed-sandwich complexes. Structure calculations were performed for CrCpTp, [VCpTp](+), and CoCpTp which show substantial distortions from ideal axial symmetry in their crystal structures. The origins of these distortions were confirmed to arise from unequal occupancy of near-degenerate delta- and pi-levels.

Journal Article↗
PubMed2004

Structural characterization of imazalil/beta-cyclodextrin inclusion complex.

An equimolar inclusion complex between imazalil, a selected fungicide, and beta-cyclodextrin using an aqueous standard solution procedure has been obtained. The complex has been investigated in solution by (1)H and (13)C NMR techniques in combination with computational methods in order to establish a valuable analytical protocol through which to gain insight into the interactions of the inclusion complex in aqueous solution. Intramolecular NMR distance constraints have been detected and used for three-dimensional complex structure determination.

Cyclodextrins↗
PubMed2000

A DNA enzyme with N-glycosylase activity.

In vitro evolution was used to develop a DNA enzyme that catalyzes the site-specific depurination of DNA with a catalytic rate enhancement of about 10(6)-fold. The reaction involves hydrolysis of the N-glycosidic bond of a particular deoxyguanosine residue, leading to DNA strand scission at the apurinic site. The DNA enzyme contains 93 nucleotides and is structurally complex. It has an absolute requirement for a divalent metal cation and exhibits optimal activity at about pH 5. The mechanism of the reaction was confirmed by analysis of the cleavage products by using HPLC and mass spectrometry. The isolation and characterization of an N-glycosylase DNA enzyme demonstrates that single-stranded DNA, like RNA and proteins, can form a complex tertiary structure and catalyze a difficult biochemical transformation. This DNA enzyme provides a new approach for the site-specific cleavage of DNA molecules.

Catalysis↗
PubMed2006

A variation of the translation attenuation model can explain the inducible regulation of the pBC16 tetracycline resistance gene in Bacillus subtilis.

Expression of the tet resistance gene from plasmid pBC16 is induced by the antibiotic tetracycline, and induction is independent of the native promoter for the gene. The nucleotide sequence at the 5' end of the tet mRNA (the leader region) is predicted to assume a complex secondary structure that sequesters the ribosome binding site for the tet gene. A spontaneous, constitutively expressed tet gene variant contains a mutation predicted to provide the tet gene with a nonsequestered ribosome binding site. Lastly, comparable levels of tet mRNA can be demonstrated in tetracycline-induced and uninduced cells. These results are consistent with the idea that the pBC16 tet gene is regulated by translation attenuation, a model originally proposed to explain the inducible regulation of the cat and erm genes in gram-positive bacteria. As with inducible cat and erm genes, the pBC16 tet gene is preceded by a translated leader open reading frame consisting of a consensus ribosome binding site and an ATG initiation codon, followed by 19 sense codons and a stop codon. Mutations that block translation of cat and erm leaders prevent gene expression. In contrast, we show that mutations that block translation of the tet leader result in constitutive expression. We provide evidence that translation of the tet leader peptide coding region blocks tet expression by preventing the formation of a secondary-structure complex that would, in the absence of leader translation, expose the tet ribosome binding site. Tetracycline is proposed to induce tet by blocking or slowing leader translation. The results indicate that tet regulation is a variation of the translation attenuation model.

Amino Acid Sequence↗
PubMed1999

Unexpected modes of PDZ domain scaffolding revealed by structure of nNOS-syntrophin complex.

The PDZ protein interaction domain of neuronal nitric oxide synthase (nNOS) can heterodimerize with the PDZ domains of postsynaptic density protein 95 and syntrophin through interactions that are not mediated by recognition of a typical carboxyl-terminal motif. The nNOS-syntrophin PDZ complex structure revealed that the domains interact in an unusual linear head-to-tail arrangement. The nNOS PDZ domain has two opposite interaction surfaces-one face has the canonical peptide binding groove, whereas the other has a beta-hairpin "finger." This nNOS beta finger docks in the syntrophin peptide binding groove, mimicking a peptide ligand, except that a sharp beta turn replaces the normally required carboxyl terminus. This structure explains how PDZ domains can participate in diverse interaction modes to assemble protein networks.

Amino Acid Sequence↗
PubMed2006

Geometry, chemical bonding, and electronic spectra of Si(n) and Si(n)-glycine (n = 3-5) complexes.

Structures and spectra are calculated for Si(n) and Si(n)-Gly (n = 3-5) complexes. Relative stability differences of Gly conformers are magnified by interactions with the Si(n) cluster, so that one conformer of Si(n)-Gly is stabilized. Significant charge transfer occurs from the amino group in Gly to a Si atom in the cluster. Interactions with Gly are predicted to shift the excitation energies of Si(n) significantly to the blue to 2.1-2.7 eV, although they are still lower than in a Si cluster passivated by hydrogen.

Electrons↗
PubMed2006

Nucleotide-dependent conformational changes in the DnaA-like core of the origin recognition complex.

Structural details of initiator proteins for DNA replication have provided clues to the molecular events in this process. EM reconstructions of the Drosophila melanogaster origin recognition complex (ORC) reveal nucleotide-dependent conformational changes in the core of the complex. All five AAA+ domains in ORC contain a conserved structural element that, in DnaA, promotes formation of a right-handed helix, indicating that helical AAA+ substructures may be a feature of all initiators. A DnaA helical pentamer can be docked into ORC, and the location of Orc5 uniquely positions this core. The results suggest that ATP-dependent conformational changes observed in ORC derive from reorientation of the AAA+ domains. By analogy to the DNA-wrapping activity of DnaA, we posit that ORC together with Cdc6 prepares origin DNA for helicase loading through mechanisms related to the established pathway of prokaryotes.

Adenosine Triphosphate↗
PubMed2002

Beyond tandem repeats: complex pattern structures and distant regions of similarity.

MOTIVATION: Tandem repeats (TRs) are associated with human disease, play a role in evolution and are important in regulatory processes. Despite their importance, locating and characterizing these patterns within anonymous DNA sequences remains a challenge. In part, the difficulty is due to imperfect conservation of patterns and complex pattern structures. We study recognition algorithms for two complex pattern structures: variable length tandem repeats (VLTRs) and multi-period tandem repeats (MPTRs). RESULTS: We extend previous algorithmic research to a class of regular tandem repeats (RegTRs). We formally define RegTRs, as well as two important subclasses: VLTRs and MPTRs. We present algorithms for identification of TRs in these classes. Furthermore, our algorithms identify degenerate VLTRs and MPTRs: repeats containing substitutions, insertions and deletions. To illustrate our work, we present results of our analysis for two difficult regions in cattle and human data which reflect practical occurrences of these subclasses in GenBank sequence data. In addition, we show the applicability of our algorithmic techniques for identifying Alu sequences, gene clusters and other distant regions of similarity. We illustrate this with an example from yeast chromosome I.

Algorithms↗
PubMed2006

Deconvolution of fluorescence spectra: contribution to the structural analysis of complex molecules.

Fluorescence spectroscopy is a sensitive analytical tool in the studies of both simple and complex molecular structures. In complex molecules, however, determining the number and position of components may give a specific insight into the structure, complementary to the other analytical techniques. We applied log-normal model to analyze fluorescence of simple monofluorophore molecule. In order to analyze spectra where both fluorophores and Raman emission bands were present, we developed a method obtained by combination of the symmetric, Gaussian, for Raman and asymmetric, log-normal model, for fluorescence, applicable to the molecules of different complexity. Technically, for each sample we varied excitation wavelength with 5 nm step and recorded the corresponding emission spectra. They were subsequently used for component analysis. Position of each component was plotted against the excitation wavelength. Applying this approach we could identify minimal number of components having stable positions, while their approximate probability density (APD) in a spectral series was correlated with the probable number of fluorophores in the molecule. The method was tested on molecules containing different number of fluorophores: monomers involved in the synthesis of plant polymer lignin-coniferyl alcohol (one fluorophore), ferulic acid (two fluorophores) and on lignin model compound produced from these monomers (many fluorophores). All investigated species belong to benzene-substituted class of compounds, and it is reasonable to assume that they have similar fluorescence band contour. We also report the results of environmental scanning electron microscopy (ESEM) studies showing multilayered dehydrogenative polymer (DHP) structure, in order to show complexity of the polymer. Our results present complementarity of these two approaches in the structural studies of the lignin model compound.

Biopolymers↗
PubMed2006

Interplay between function and structure in complex networks.

We show that abrupt structural transitions can arise in functionally optimal networks, driven by small changes in the level of transport congestion. Our results offer an explanation as to why so many diverse species of network structure arise in nature (e.g., fungal systems) under essentially the same environmental conditions. Our findings are based on an exactly solvable model system which mimics a variety of biological and social networks. We then extend our analysis by introducing a renormalization scheme involving cost motifs, to describe analytically the average shortest path across multiple-ring-and-hub networks. As a consequence, we uncover a "skin effect" whereby the structure of the inner multi-ring core can cease to play any role in terms of determining the average shortest path across the network.

Journal Article↗
PubMed1997

Copper(II) Complexes of N,N'-Bis((2-substituted-imidazol-4-yl)methylene)-3,3'-diaminodi- propylamine (2-Substituent = H, Me): Delta and Lambda Enantiomorphs of the Protonated Complex and Helical Structure of the Deprotonated Complex Formed by Hydrogen Bonds.

Copper(II) complexes with the quinquedentate ligands H(2)L(n)() (n = 1, 2) of the 1:2 condensation products of 3,3'-diaminodipropylamine and each of 4-formylimidazole and 4-formyl-2-methylimidazole have been synthesized and characterized, where the complexes have the general formula of [Cu(H(2)L(n)())]X(2) and are abbreviated as 1X(2), and 2X(2) (n = 1, 2 for 2-substituent = H, Me; X = ClO(4), NO(3), Cl). X-ray crystal structures of 1(NO(3))(2), and 2(Cl)(2) were determined: 1(NO(3))(2), monoclinic, space group P2(1)/c (No. 14), a = 9.610(4) Å, b = 13.463(5) Å, c = 15.568(5) Å, beta = 98.12(3) degrees, and Z = 4; 2(Cl)(2), monoclinic, space group P2(1)/n (No. 14), a = 9.884(2) Å, b = 15.073(3) Å, c = 15.295(2) Å, beta = 98.57(2) degrees, and Z = 4. The complex assumes Delta or Lambda enantiomorphs due to the spiral arrangement of the quinquedentate ligand around the copper(II) ion, and these Delta and Lambda enantiomorphs of the cation for 1(NO(3))(2) and 2(Cl)(2) coexist as the racemic form in the crystals. When the protonated complexes were treated with NaOH, the mono-deprotonated complexes with the formula [CuHL(n)()]ClO(4), 1'ClO(4) (n = 1) and 2'ClO(4) (n = 2), were obtained. Crystal data for 1'ClO(4): Pbca (No. 61) with a = 13.211(3) Å, b = 25.387(3) Å, c = 10.939(3) Å, and Z = 8.; 2'.ClO(4), Pbca (No. 61) with a = 16.554(4) Å, b = 20.609(4) Å, c = 12.423(3) Å, and Z = 8. The structures consist of an electronically monopositive copper(II) complex involving a deprotonated imidazole moiety and a protonated imidazole moiety per molecular unit and a mononegative anion ClO(4)(-), where an imidazolate nitrogen atom N(2) of the copper(II) complex is hydrogen bonded to the imidazole nitrogen atom N(6) ( denotes the symmetry operation of (1)/(2) + x, (1)/(2) - y, -z) of the adjacent unit with the hydrogen bond distance of N(2).N(6) of 2.842(6) for 1'ClO(4) and 2.815(4) Å for 2'ClO(4) to give a one-dimensional helical structure running along the a-axis. Through the hydrogen bonds, the Delta isomer only aggregates with the Delta isomer and the Lambda isomer only aggregates with the Lambda isomer to give an extended helical chain structure described as DeltaDeltaDeltaDeltaDelta. or LambdaLambdaLambdaLambdaLambda., respectively.

Journal Article↗
PubMed2005

Effects of complexation with 18-crown-6 on the hypernucleofugality of phenyl-lambda3-iodanyl groups. Synthesis of vinyl-lambda3-iodane.18-crown-6 complex.

[structure: see text] 4-tert-Butyl-1-cyclohexenyl(phenyl)(tetrafluoroborato)-lambda(3)-iodane forms a discrete supramolecular complex by the reaction with 18-crown-6. Solvolysis of the cyclohexenyl-lambda(3)-iodane in the presence of 18-crown-6 indicates that the complexation with 18-crown-6 tends to decrease the leaving group ability of hypervalent phenyl-lambda(3)-iodanyl groups.

Journal Article↗